Chloroplast genome sequencing of Carya Illinoinensis cv. Xinxuan-4, a new pecan pollinated cultivar

Abstract

Carya illinoinensis, is a highly valuable nut plant that is cultivated worldwide. As a precious pecan pollination resource, C. illinoinensis cv. Xinxuan-4 is protandrous, with a very early bud break in China. In this study, the chloroplast (cp) genome of 'Xinxuan-4' was sequenced and compared with closely related cultivars. The cp genome was found to be 160,819 bp in length, and it had a common quadripartite architecture with one large single copy (LSC; 90,022 bp), one small single copy (SSC; 18,791 bp), and two inverted repeats (IRs; 26,003 bp). The genome contained 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes, with a GC content of 36.1%. Furthermore, 278 simple sequence repeats and 59 long repeat sequences were identified, and the genome comparisons revealed that there was a greater divergence in the noncoding regions than in the coding regions. According to the gene selective pressure analysis, five genes (petD, rpl16, rps12, rpoC2, and rpoC1) were identified to be potentially under positive selection when contrasted with the other Carya genotypes. Phylogenetic analysis of the cp genome of 'Xinxuan-4' and 17 other species inferred that Carya is monophyletic and that the genetic relationship between 'Xinxuan-4' and 'Pawnee' is quite close from an evolutionary perspective. The currently characterized cp genome of 'Xinxuan-4' offers useful data for subsequent research on this pecan species.

Keywords

• pecan
• chloroplast
• genome comparison
• phylogenetic analysis